+Open data
-Basic information
Entry | Database: PDB / ID: 7aqc | |||||||||
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Title | Structure of the bacterial RQC complex (Decoding State) | |||||||||
Components |
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Keywords | RIBOSOME / rqch / rqc / rqc2 / hsp15 / fibronectin-binding protein / NEMF / ribosome-associated quality control / ribosome-associated / 50s / Alanine-tailing | |||||||||
Function / homology | Function and homology information RQC complex / positive regulation of rRNA processing / nucleoid / ribosomal large subunit binding / rescue of stalled ribosome / rRNA processing / large ribosomal subunit / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding ...RQC complex / positive regulation of rRNA processing / nucleoid / ribosomal large subunit binding / rescue of stalled ribosome / rRNA processing / large ribosomal subunit / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / response to antibiotic / mRNA binding / DNA binding / RNA binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Bacillus subtilis subsp. subtilis str. 168 (bacteria) Bacillus subtilis (bacteria) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.99 Å | |||||||||
Authors | Filbeck, S. / Pfeffer, S. | |||||||||
Funding support | Germany, United States, 2items
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Citation | Journal: Mol Cell / Year: 2021 Title: Mimicry of Canonical Translation Elongation Underlies Alanine Tail Synthesis in RQC. Authors: Sebastian Filbeck / Federico Cerullo / Helge Paternoga / George Tsaprailis / Claudio A P Joazeiro / Stefan Pfeffer / Abstract: Aborted translation produces large ribosomal subunits obstructed with tRNA-linked nascent chains, which are substrates of ribosome-associated quality control (RQC). Bacterial RqcH, a widely conserved ...Aborted translation produces large ribosomal subunits obstructed with tRNA-linked nascent chains, which are substrates of ribosome-associated quality control (RQC). Bacterial RqcH, a widely conserved RQC factor, senses the obstruction and recruits tRNA to modify nascent-chain C termini with a polyalanine degron. However, how RqcH and its eukaryotic homologs (Rqc2 and NEMF), despite their relatively simple architecture, synthesize such C-terminal tails in the absence of a small ribosomal subunit and mRNA has remained unknown. Here, we present cryoelectron microscopy (cryo-EM) structures of Bacillus subtilis RQC complexes representing different Ala tail synthesis steps. The structures explain how tRNA is selected via anticodon reading during recruitment to the A-site and uncover striking hinge-like movements in RqcH leading tRNA into a hybrid A/P-state associated with peptidyl-transfer. Finally, we provide structural, biochemical, and molecular genetic evidence identifying the Hsp15 homolog (encoded by rqcP) as a novel RQC component that completes the cycle by stabilizing the P-site tRNA conformation. Ala tailing thus follows mechanistic principles surprisingly similar to canonical translation elongation. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7aqc.cif.gz | 2.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7aqc.ent.gz | 1.6 MB | Display | PDB format |
PDBx/mmJSON format | 7aqc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7aqc_validation.pdf.gz | 980.2 KB | Display | wwPDB validaton report |
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Full document | 7aqc_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 7aqc_validation.xml.gz | 128.5 KB | Display | |
Data in CIF | 7aqc_validation.cif.gz | 229.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aq/7aqc ftp://data.pdbj.org/pub/pdb/validation_reports/aq/7aqc | HTTPS FTP |
-Related structure data
Related structure data | 11862MC 7aqdC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-RNA chain , 3 types, 4 molecules ABPT
#1: RNA chain | Mass: 914625.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) |
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#2: RNA chain | Mass: 36157.520 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: GenBank: 1150402534 |
#15: RNA chain | Mass: 24491.547 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) |
+50S ribosomal protein ... , 27 types, 27 molecules CDEFGIJKLMNOQSUVXZabcdefghi
-Protein , 2 types, 2 molecules RY
#17: Protein | Mass: 65307.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: O34693 |
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#23: Protein | Mass: 9737.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: P37557 |
-Protein/peptide , 1 types, 1 molecules W
#21: Protein/peptide | Mass: 515.560 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Bacterial RQC complex / Type: RIBOSOME / Entity ID: all / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN |
Image recording | Electron dose: 45 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
EM imaging optics | Energyfilter slit width: 20 eV |
-Processing
Software | Name: PHENIX / Version: 1.18.2_3874: / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 5869410 | ||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.99 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 138382 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building |
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Refine LS restraints |
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